A Victoria Police spokeswoman said the force had met with the Office of the Disability Services Commissioner and would conduct a "full investigation".

Meanwhile, the Department of Human Services is separately reviewing the organisation after a serious incident at the site, flagging it could slash Aspect's $4.8 million state government funding if adverse findings are made in any investigation.

On Wednesday, the Victorian government said it was "gravely concerned" by allegations against Aspect and described abuse of vulnerable people as appalling.

"The government will not hesitate to take the strongest action against anyone who has been involved in abusive behaviour in our disability care system," a spokesman for Disability Minister Martin Foley said.

"Victoria Police is investigating these matters and as such, it would be inappropriate to comment further."

Aspect chief executive Adrian Ford said the company would cooperate fully with police. "We have nothing to hide," he said.

"Aspect has not been informed of any allegations uncovered by the Disability Services Commission that warrant police investigation."

In a statement last week, Mr Ford moved to distance Aspect from the box scandal, saying the company had just recently taken over the site from its former operator, Alpha Autism. He said the "desensitising​" box was removed within 24 hours of head office becoming aware.

Fairfax Media has confirmed the box was removed five months after Aspect assumed full responsibility from Alpha.

Aspect said its own investigation found there was no evidence the purpose-built box was used on a client.

The organisation has not apologised for the box or for failing to report it to authorities after quietly destroying it in April.

Mr Ford said people with autism sometimes experienced challenges with sensory overload and may choose to remove themselves to a quiet place. But the box at Heatherton was "in no way, shape or form suitable for its purpose", he said.

Following revelations by Fairfax Media the Department of Human Services was instructed to also begin inquiring into the box matter, while its wide-ranging review into Aspect continued.

"The department has a current quality-of-support review in progress and will work with Victoria Police to ensure this does not impact on their investigations," a DHS spokesman said on Wednesday.

The Disability Services Commissioner said it had initiated four investigations in the past 12 months, two relating to allegations of abuse and two involving service quality.

The commissioner is prohibited from commenting on specific investigations.